Anomaly detection is considered a very important task for hyperspectral data exploitation. It is now routinely applied in many application domains, including defence and intelligence, public safety, precision agriculture, geology, or forestry. Many of these applications require timely responses for swift decisions which depend upon high computing performance of algorithm analysis. However, with the recent explosion in the amount and dimensionality of hyperspectral imagery, this problem calls for the incorporation of parallel computing techniques. In the past, clusters of computers have offered an attractive solution for fast anomaly detection in hyperspectral data sets already transmitted to Earth. However, these systems are expensive and difficult to adapt to on-board data processing scenarios, in which low-weight and low-power integrated components are essential to reduce mission payload and obtain analysis results in (near) real-time, i.e., at the same time as the data is collected by the sensor. An exciting new development in the field of commodity computing is the emergence of commodity graphics processing units (GPUs), which can now bridge the gap towards on-board processing of remotely sensed hyperspectral data. In this paper, we develop a new morphological algorithm for anomaly detection in hyperspectral images along with an efficient GPU implementation of the algorithm. The algorithm is implemented on latest-generation GPU architectures, and evaluated with regards to other anomaly detection algorithms using hyperspectral data collected by NASA’s Airborne Visible Infra-Red Imaging Spectrometer (AVIRIS) over the World Trade Center (WTC) in New York, five days after the terrorist attacks that collapsed the two main towers in the WTC complex. The proposed GPU implementation achieves real-time performance in the considered case study.